Re: [AMBER] stapled peptide- PDB bond atom problem

From: David A Case <>
Date: Mon, 3 Dec 2018 13:17:07 -0500

On Mon, Dec 03, 2018, Angew Chemie wrote:
>> lnk = loadpdb LNK1_PEP_LNK2.pdb

First, it looks like you never loaded any library files.

You need to have commands like this in your tleap script:

LIG = loadMol2 <mol2-file-name>

Second, your pdb files have blank residues names (which is not legal).
GaussView is not creating PDB files that look much like what PDB files are
supposed to look like.

>Loading PDB file: ./LNK1_PEP_LNK2.pdb
>-- residue 2: duplicate [ C] atoms (total 5)
>-- residue 2: duplicate [ H] atoms (total 9)
>-- residue 2: duplicate [ N] atoms (total 2)


Third, atom names within a residue must be unique. Also, the atom names
in the PDB file must exactly match those in the mol2 or off files you

So compare the atom names in your PDB files with those in the library
files you created; edit the PDB files so that the atom and residue names
match up.

...good luck....dac

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Received on Mon Dec 03 2018 - 10:30:02 PST
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